Research workbench
X-ray crystal structure of canine myeloperoxidase at 3 ångströms resolution
Analyse X-ray crystal structure of canine myeloperoxidase at 3 ångströms resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MYP
- Type
- protein
- Length
- 1,132 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myeloperoxidase
- EC
- 1.11.1.7
- UniProt
- P05164
- Ligands
- HEM, NAG, CA
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Myeloperoxidase (EC 1.11.1.7) | protein | 104 | 25% helix, 11% strand | P05164 |
| C, D | Myeloperoxidase (EC 1.11.1.7) | protein | 462 | 36% helix, 6% strand | P05164 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, C, B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains C, D, B, A
- CA · Calcium ion · metal · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.80 | 0.82 | 67 | HEM |
| 2 | 831 | 0.80 | 0.82 | 76 | empty |
| 3 | 749 | 0.79 | 0.83 | 67 | HEM |
| 4 | 53 | 0.69 | 0.97 | 18 | empty |
| 5 | 90 | 0.49 | 0.82 | 20 | empty |
Interfaces
6 interfaces between chains.
- B–D · 5639 Ų buried · 95 hydrogen bonds · protein-protein
- A–C · 5628 Ų buried · 108 hydrogen bonds · protein-protein
- A–B · 629 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 345 Ų buried · 3 hydrogen bonds · protein-protein
- C–B · 250 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 1MYP · X-ray crystal structure of canine myeloperoxidase at 3 ångströms resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P05164 · AlphaFold monomer V2.0 prediction for myeloperoxidase (P05164) · a predicted model of the same protein · chain C against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P05164
- Elsewhere: RCSB PDB 1MYP · PDBe 1MYP · UniProt P05164
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